Research workbench
Crystal structure of full-length human DCAF15-DDB1(DELTABPB)-DDA1- RBM39 in complex with indisulam
Analyse Crystal structure of full-length human DCAF15-DDB1(DELTABPB)-DDA1- RBM39 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UD7
- Type
- protein
- Length
- 1,386 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DDB1- and CUL4-associated factor 15; DNA damage-binding protein 1,DNA damage-binding…
- UniProt
- Q66K64, Q16531, Q7Z3L0, Q9BW61
- Ligands
- EF6
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DDB1- and CUL4-associated factor 15 | protein | 426 | 11% helix, 39% strand | Q66K64 |
| B | DNA damage-binding protein 1,DNA damage-binding protein 1 | protein | 806 | 6% helix, 52% strand | Q16531 |
| C | RNA-binding motif protein 39 | protein | 81 | 27% helix, 38% strand | Q7Z3L0 |
| D | DET1- and DDB1-associated protein 1 | protein | 73 | 21% helix, 10% strand | Q9BW61 |
Ligands and binding sites
- EF6 · N~1~-(3-chloro-1H-indol-7-yl)benzene-1,4-disulfonamide · ligand · chains A, C
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 585 | 0.84 | 0.89 | 75 | empty |
| 2 | 831 | 0.83 | 0.86 | 95 | EF6 |
| 3 | 504 | 0.80 | 0.87 | 69 | empty |
| 4 | 553 | 0.76 | 0.83 | 73 | empty |
| 5 | 102 | 0.73 | 0.94 | 30 | GOL |
Interfaces
4 interfaces between chains.
- B–D · 3103 Ų buried · 48 hydrogen bonds · protein-protein
- A–B · 2445 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 1312 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 762 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6UD7 · Crystal structure of full-length human DCAF15-DDB1(deltaBPB)-DDA1-RBM39 in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q16531 · AlphaFold monomer V2.0 prediction for DNA damage-binding protein 1 (Q16531) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q66K64 · AlphaFold monomer V2.0 prediction for DDB1- and CUL4-associated factor 15 (Q66K64) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q9BW61 · AlphaFold monomer V2.0 prediction for DET1- and DDB1-associated protein 1 (Q9BW61) · a predicted model of the same protein · chain D against A, TM-score 0.30
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q66K64
- Every structure of UniProt Q16531
- Every structure of UniProt Q7Z3L0
- Every structure of UniProt Q9BW61
- Elsewhere: RCSB PDB 6UD7 · PDBe 6UD7 · UniProt Q66K64 · UniProt Q16531 · UniProt Q7Z3L0 · UniProt Q9BW61
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